DGKB

diacylglycerol kinase beta, the group of Diacylglycerol kinases|EF-hand domain containing

Basic information

Region (hg38): 7:14145049-14974777

Previous symbols: [ "DAGK2" ]

Links

ENSG00000136267 ∙ NCBI:1607 ∙ OMIM:604070 ∙ HGNC:2850 ∙ Uniprot:Q9Y6T7 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the DGKB gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the DGKB gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			23			23
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	23	0	0

Variants in DGKB

This is a list of pathogenic ClinVar variants found in the DGKB region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
7-14149208-T-C		not specified	Uncertain significance (Apr 22, 2022)
7-14149217-G-T		not specified	Uncertain significance (Mar 18, 2024)
7-14176894-C-T		not specified	Uncertain significance (Jul 06, 2021)
7-14178047-A-C		not specified	Uncertain significance (Jun 22, 2023)
7-14338538-T-C		not specified	Uncertain significance (Dec 22, 2023)
7-14338591-A-T		not specified	Uncertain significance (Nov 09, 2024)
7-14338608-T-C		not specified	Uncertain significance (Nov 27, 2024)
7-14574296-C-A		not specified	Uncertain significance (Oct 26, 2021)
7-14574332-A-C		not specified	Uncertain significance (Nov 29, 2023)
7-14580883-T-C		not specified	Uncertain significance (Sep 28, 2022)
7-14580939-A-G		not specified	Uncertain significance (Mar 26, 2024)
7-14583134-T-A		not specified	Uncertain significance (May 30, 2024)
7-14607486-G-C		not specified	Uncertain significance (Aug 17, 2022)
7-14621393-A-T		not specified	Uncertain significance (Apr 15, 2024)
7-14621413-C-T		not specified	Uncertain significance (Feb 21, 2024)
7-14621428-T-C		not specified	Uncertain significance (Oct 17, 2023)
7-14682641-T-A			Uncertain significance (Feb 08, 2023)
7-14682763-C-T		not specified	Likely benign (May 13, 2024)
7-14694114-C-T		not specified	Uncertain significance (Mar 12, 2024)
7-14698108-G-C		not specified	Uncertain significance (Feb 05, 2024)
7-14701685-C-T		not specified	Uncertain significance (Apr 08, 2022)
7-14718628-G-A		not specified	Uncertain significance (Oct 17, 2023)
7-14718646-G-A		not specified	Uncertain significance (Mar 16, 2022)
7-14718649-C-T		not specified	Uncertain significance (May 04, 2022)
7-14718665-C-T		not specified	Uncertain significance (Mar 20, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
DGKB	protein_coding	protein_coding	ENST00000403951	25	829729

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.530	0.470	125009	0	11	125020	0.0000440

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.95	296	406	0.728	0.0000207	5259
Missense in Polyphen		64	147.24	0.43466		1916
Synonymous	-0.824	150	138	1.09	0.00000716	1419
Loss of Function	4.92	10	46.0	0.218	0.00000235	590

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000896	0.0000896
Ashkenazi Jewish	0.0000995	0.0000993
East Asian	0.0000552	0.0000550
Finnish	0.00	0.00
European (Non-Finnish)	0.0000357	0.0000353
Middle Eastern	0.0000552	0.0000550
South Asian	0.0000656	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Exhibits high phosphorylation activity for long-chain diacylglycerols. {ECO:0000250}.
• Pathway: Glycerolipid metabolism - Homo sapiens (human);Glycerophospholipid metabolism - Homo sapiens (human);Choline metabolism in cancer - Homo sapiens (human);Phosphatidylinositol signaling system - Homo sapiens (human);Phospholipase D signaling pathway - Homo sapiens (human);Signaling by GPCR;Signal Transduction;Effects of PIP2 hydrolysis;Platelet activation, signaling and aggregation;Glycerophospholipid metabolism;Hemostasis;G alpha (q) signalling events;GPCR downstream signalling (Consensus)

Recessive Scores

• pRec: 0.127

Intolerance Scores

• rvis_EVS: -0.93
• rvis_percentile_EVS: 9.61

Haploinsufficiency Scores

• pHI: 0.178
• hipred: Y
• hipred_score: 0.601
• ghis: 0.550

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.958

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Dgkb
• Phenotype: nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); homeostasis/metabolism phenotype

Gene ontology

• Biological process: protein kinase C-activating G protein-coupled receptor signaling pathway;response to bacterium;platelet activation;intracellular signal transduction;diacylglycerol metabolic process;glycerolipid metabolic process;lipid phosphorylation;modulation of chemical synaptic transmission;regulation of postsynapse organization
• Cellular component: cytoplasm;plasma membrane;Schaffer collateral - CA1 synapse;glutamatergic synapse
• Molecular function: NAD+ kinase activity;diacylglycerol kinase activity;calcium ion binding;ATP binding